pymdkit 1.2.1__tar.gz → 1.2.3__tar.gz

{pymdkit-1.2.1/src/pymdkit.egg-info → pymdkit-1.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.1
+Version: 1.2.3
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -16,6 +16,7 @@ License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: ase
 Requires-Dist: pymatgen
+Requires-Dist: mp-api
 Requires-Dist: pyxtal
 Requires-Dist: dpdata
 Dynamic: license-file
@@ -41,7 +42,7 @@ pip install pymdkit
 ```
 
 This installs the `pymdkit` command into the active conda environment, together
-with its direct dependencies (numpy, ase, pymatgen, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
+with its direct dependencies (numpy, ase, pymatgen, mp-api, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.1 → pymdkit-1.2.3}/README.md

@@ -19,7 +19,7 @@ pip install pymdkit
 ```
 
 This installs the `pymdkit` command into the active conda environment, together
-with its direct dependencies (numpy, ase, pymatgen, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
+with its direct dependencies (numpy, ase, pymatgen, mp-api, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.1 → pymdkit-1.2.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.1"
+version = "1.2.3"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"
@@ -26,7 +26,8 @@ classifiers = [
 dependencies = [
     "numpy",
     "ase",
-    "pymatgen",
+    "pymatgen",
+    "mp-api",
     "pyxtal",
     "dpdata",
 ]

{pymdkit-1.2.1 → pymdkit-1.2.3}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.1"
+__version__ = "1.2.3"

pymdkit-1.2.3/src/pymdkit/commands/stable_entry.py

@@ -0,0 +1,116 @@
+"""Download stable Materials Project structures for a chemical system."""
+
+from __future__ import annotations
+
+import argparse
+import re
+from itertools import combinations
+from dataclasses import dataclass
+from pathlib import Path
+
+COMMAND = "stable-entry"
+HELP = "Download stable Materials Project structures for a chemical system."
+
+
+@dataclass
+class StableStructure:
+    material_id: str
+    formula: str
+    structure: object
+
+
+def safe_formula(formula):
+    return re.sub(r"[^A-Za-z0-9_.-]+", "", str(formula))
+
+
+def doc_get(doc, name, default=None):
+    if isinstance(doc, dict):
+        return doc.get(name, default)
+    return getattr(doc, name, default)
+
+
+def normalize_doc(doc):
+    material_id = str(doc_get(doc, "material_id", "unknown"))
+    formula = doc_get(doc, "formula_pretty") or doc_get(doc, "formula")
+    structure = doc_get(doc, "structure")
+    if formula is None and structure is not None:
+        formula = structure.composition.reduced_formula
+    if structure is None:
+        raise ValueError(f"MP document {material_id} has no structure field")
+    return StableStructure(material_id=material_id, formula=str(formula), structure=structure)
+
+
+def entry_sort_key(entry):
+    return (len(entry.structure.composition.elements), entry.formula, entry.material_id)
+
+
+def add_arguments(parser: argparse.ArgumentParser) -> None:
+    parser.add_argument("-s", nargs="+", required=True,
+                        help="Chemical system elements, e.g. -s Li La Ta Cl.")
+    parser.add_argument("-mp-api-key", default=None,
+                        help="Materials Project API key.")
+
+
+def subsystem_labels(elements):
+    """Return all subsystem labels needed to build the full chemsys hull."""
+    labels = []
+    for size in range(1, len(elements) + 1):
+        for subset in combinations(elements, size):
+            labels.append("-".join(subset))
+    return labels
+
+
+def fetch_stable_structures(elements, api_key=None):
+    from mp_api.client import MPRester
+
+    fields = ["material_id", "formula_pretty", "structure"]
+    by_mpid = {}
+    with MPRester(api_key) as mpr:
+        for chemsys in subsystem_labels(elements):
+            docs = mpr.materials.summary.search(
+                chemsys=chemsys,
+                is_stable=True,
+                fields=fields,
+            )
+            for doc in docs:
+                entry = normalize_doc(doc)
+                by_mpid[entry.material_id] = entry
+    return list(by_mpid.values())
+
+
+def run(args) -> int:
+    from pymatgen.io.cif import CifWriter
+
+    elements = list(dict.fromkeys(args.s))
+    label = "-".join(elements)
+    out_dir = Path(f"{label}-stable-entries")
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    try:
+        entries = fetch_stable_structures(elements, args.mp_api_key)
+    except ModuleNotFoundError as exc:
+        if exc.name == "mp_api":
+            raise SystemExit(
+                "Error: stable-entry requires mp-api. Reinstall pymdkit 1.2.3+ "
+                "or run `pip install mp-api`."
+            ) from exc
+        raise
+
+    entries = sorted(entries, key=entry_sort_key)
+    written = 0
+    for entry in entries:
+        mpid = safe_formula(entry.material_id)
+        formula = safe_formula(entry.formula)
+        path = out_dir / f"{mpid}-{formula}.cif"
+        CifWriter(entry.structure).write_file(str(path))
+        print(f"{mpid}\t{entry.formula}\t-> {path}")
+        written += 1
+
+    print(f"Wrote {written} stable entr{'y' if written == 1 else 'ies'} to {out_dir}")
+    return 0 if written else 1
+
+
+if __name__ == "__main__":
+    _parser = argparse.ArgumentParser(description=__doc__)
+    add_arguments(_parser)
+    raise SystemExit(run(_parser.parse_args()))

{pymdkit-1.2.1 → pymdkit-1.2.3/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.1
+Version: 1.2.3
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -16,6 +16,7 @@ License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: ase
 Requires-Dist: pymatgen
+Requires-Dist: mp-api
 Requires-Dist: pyxtal
 Requires-Dist: dpdata
 Dynamic: license-file
@@ -41,7 +42,7 @@ pip install pymdkit
 ```
 
 This installs the `pymdkit` command into the active conda environment, together
-with its direct dependencies (numpy, ase, pymatgen, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
+with its direct dependencies (numpy, ase, pymatgen, mp-api, pyxtal, dpdata). Some of these packages may install their own transitive dependencies.
 
 Verify:
 

{pymdkit-1.2.1 → pymdkit-1.2.3}/src/pymdkit.egg-info/requires.txt

@@ -1,5 +1,6 @@
 numpy
 ase
 pymatgen
+mp-api
 pyxtal
 dpdata

pymdkit-1.2.1/src/pymdkit/commands/stable_entry.py

@@ -1,77 +0,0 @@
-"""Download stable Materials Project entries for a chemical system."""
-
-from __future__ import annotations
-
-import argparse
-import re
-from pathlib import Path
-
-COMMAND = "stable-entry"
-HELP = "Download stable Materials Project structures for a chemical system."
-
-
-def safe_formula(formula):
-    return re.sub(r"[^A-Za-z0-9_.-]+", "", str(formula))
-
-
-def entry_id_text(entry):
-    entry_id = getattr(entry, "entry_id", "")
-    if isinstance(entry_id, dict):
-        for key in ("material_id", "task_id", "entry_id", "id"):
-            if entry_id.get(key):
-                return str(entry_id[key])
-        return "-".join(f"{k}-{v}" for k, v in sorted(entry_id.items()))
-    if entry_id:
-        return str(entry_id)
-    data = getattr(entry, "data", {}) or {}
-    for key in ("material_id", "task_id", "entry_id", "id"):
-        if data.get(key):
-            return str(data[key])
-    return "unknown"
-
-
-def entry_sort_key(entry):
-    formula = str(entry.composition.reduced_formula)
-    return (len(entry.composition.elements), formula, entry_id_text(entry))
-
-
-def add_arguments(parser: argparse.ArgumentParser) -> None:
-    parser.add_argument("-s", nargs="+", required=True,
-                        help="Chemical system elements, e.g. -s Li La Ta Cl.")
-    parser.add_argument("-mp-api-key", default=None,
-                        help="Materials Project API key.")
-
-
-def run(args) -> int:
-    from pymatgen.ext.matproj import MPRester
-    from pymatgen.io.cif import CifWriter
-
-    elements = list(dict.fromkeys(args.s))
-    label = "-".join(elements)
-    out_dir = Path(f"{label}-stable-entries")
-    out_dir.mkdir(parents=True, exist_ok=True)
-
-    with MPRester(args.mp_api_key) as mpr:
-        entries = mpr.get_entries_in_chemsys(
-            elements, inc_structure=True,
-            additional_criteria={"thermo_types": ["GGA_GGA+U"], "is_stable": True},
-        )
-
-    entries = sorted(entries, key=entry_sort_key)
-    written = 0
-    for entry in entries:
-        mpid = safe_formula(entry_id_text(entry).split(" ")[0])
-        formula = safe_formula(entry.composition.reduced_formula)
-        path = out_dir / f"{mpid}-{formula}.cif"
-        CifWriter(entry.structure).write_file(str(path))
-        print(f"{mpid}\t{entry.composition.reduced_formula}\t-> {path}")
-        written += 1
-
-    print(f"Wrote {written} stable entr{'y' if written == 1 else 'ies'} to {out_dir}")
-    return 0 if written else 1
-
-
-if __name__ == "__main__":
-    _parser = argparse.ArgumentParser(description=__doc__)
-    add_arguments(_parser)
-    raise SystemExit(run(_parser.parse_args()))